Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy

Abstract

The Amazon and neighboring South American river basins harbor the world’s most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of major clades within the family are inconsistent across different methodologies, and half of the extant serrasalmid genera are suggested to be non-monophyletic. We analyzed exon capture to reexamine the evolutionary relationships among 63 (of 99) species across all 16 serrasalmid genera and their nearest outgroups, including multiple individuals per species to account for cryptic lineages. To reconstruct the timeline of serrasalmid diversification, we time-calibrated this phylogeny using two different fossil-calibration schemes to account for uncertainty in taxonomy with respect to fossil teeth. Finally, we analyzed diet evolution across the family and comment on associated changes in dentition, highlighting the ecomorphological diversity within serrasalmids. We document widespread non-monophyly of genera within Myleinae, as well as between Serrasalmus and Pristobrycon, and propose that reliance on traits like teeth to distinguish among genera is confounded by ecological homoplasy, especially among herbivorous and omnivorous taxa. We clarify the relationships among all serrasalmid genera, propose new subfamily affiliations, and support hemiodontids as the sister taxon to Serrasalmidae. [Characiformes; exon capture; ichthyochory; molecular time-calibration; piscivory.]

The B Chromosomes of Prochilodus lineatus (Teleostei, Characiformes) Are Highly Enriched in Satellite DNAs

“…Among them, we found the following: (i) One 52 nt-long satDNA (PliSat26) was shared among M. macrocephalus , Characidium gomesi , and Astyanax paranae and this sequence was previously known as CharSat01-52 and is conserved within the Characiformes clade [ 41 ]; (ii) one satDNA (PliSat8) was shared with Semaprochilodus taeniurus ( Figure S2 ) and this sequence was previously characterized in the W chromosome of the referred species (known as STW4, accession number: JX157128.1; [ 46 ]) and seemed conserved in the family Prochilodontidae; (iii) eight satDNAs (PliSat12, PlisSat15, PliSat18, PliSat21, PliSat30, PliSat36, PliSat40, and PliSat43) were shared with M . macrocephalus ( Figure 3 , Figure S2 ), indicating that these tandem repeats originated before the split of Prochilodontidae and Anostomidae, which also includes two other characiform families (Chilodontidae and Curimatidae) with an approximate divergence time of 50–70 million years according to Kolmann et al [ 47 ].…”

“…However, the variant profiles provided a genome-wide view of the organization of satDNAs and revealed that six satDNAs (PliSat12, PliSat18, PliSat21, PliSat30, PliSat36, and PliSat40) did not present a fixed mutation (indel or substitution) for a specific species. In this context, even the large gaps observed in the consensus alignments (e.g., PliSat21-59/MmaSat16-51) are not fully fixed ( Figure 3 a) after millions of years of divergence [ 47 ]. Interestingly, the variant profiles of PliSat12-42/MmaSat07-42 revealed that this satDNA was highly abundant in both genomes and also exhibited a notable similarity in the SNPs.…”

“…Regarding the conservation and persistence of satDNAs between distant species, the sharing of nine satDNAs with M. macrocephalus is notable and points to the long-term persistence and conservation of these sequences over millions of years [ 47 ]. To date, the long-term evolutionary persistence of satellite DNAs is uncommon and there have been very few described cases [ 41 , 67 , 69 , 70 , 71 , 72 ] primarily because this type of sequence follows a concerted evolutionary pattern that results in high levels of intraspecies sequence homogeneity and low rates of evolutionary persistence [ 5 , 73 , 74 ].…”

Taxonomia E Filogenia De Peixes De Riachos Brasileiros

“…Entretanto, análises filogenéticas baseadas em dados morfológicos indicam como mais parcimoniosa a hipótese de uma origem independente dos dois grupos (Buckup 1998). Da mesma forma, análises moleculares recentes demonstram a proximidade filogenética entre Parodontidae e Anostomoidea (Anostomidae + Prochilodontidae + Chilodontidae + Curimatidae) (Kolmann et al 2020 e análises citadas por estes autores). Há evidências de que os três gêneros nominais tradicionalmente reconhecidos sejam monofiléticos, porém apenas as sinapomorfias do gênero Apareiodon são discutidas na literatura (Starnes & Schindler 1993).…”

“…A monofilia, posição filogenética e as interrelações entre os principais subgrupos de Cichlidae são relativamente bem estudas (e.g., Stiassny 1981, 1987, Stiassny & Jensen 1987, Casciotta & Arratia 1993, Kullander 1998, Farias et al 2000, Vences et al 2001, Sparks & Smith 2004, Smith et al 2008, McMahan et al 2013, López-Fernandez et al 2013). Novos métodos de sequenciamento genômico permitiram realizar estudos filogenéticos de grande precisão (Ilves & López-Fernandez 2014).…”